A major challenge for applications of graphene in nanoelectronics is the absence of a band gap in its low energy spectrum. One possibility of gap opening is doping and there are various methods to achieve it: evaporation, thermal treatment, and plasma doping. In this study, using ab initio molecular dynamics, we investigate graphene doping mediated by substrate-induced mechanisms. More specifically, we address graphene on a B-doped Si(100) surface. Our ab initio total energy calculations show that B atoms prefer to locate on the surface layer of Si(100). Further, intercalation of B atoms into vacancy positions of graphene is only found for temperatures larger than 700 K. In a second step, the electrical transport properties of B-doped graphene are studied using the non-equilibrium Green's function approach.